US8993292B2 - Methods and systems for differential extraction - Google Patents

Methods and systems for differential extraction Download PDF

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US8993292B2
US8993292B2 US12/117,579 US11757908A US8993292B2 US 8993292 B2 US8993292 B2 US 8993292B2 US 11757908 A US11757908 A US 11757908A US 8993292 B2 US8993292 B2 US 8993292B2
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dna
compartment
cell
sperm
certain embodiments
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US20080281089A1 (en
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Yingjie Liu
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Applied Biosystems LLC
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Applied Biosystems LLC
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Priority claimed from US12/015,414 external-priority patent/US20080176320A1/en
Priority claimed from US12/032,270 external-priority patent/US8017332B2/en
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Priority to US12/117,579 priority Critical patent/US8993292B2/en
Priority to CA002686842A priority patent/CA2686842A1/fr
Priority to BRPI0811304-1A2A priority patent/BRPI0811304A2/pt
Priority to CN200880023150.7A priority patent/CN101796179A/zh
Priority to EP08755249A priority patent/EP2144993A4/fr
Priority to PCT/US2008/063273 priority patent/WO2008141203A1/fr
Priority to JP2010507701A priority patent/JP2010527442A/ja
Priority to AU2008251401A priority patent/AU2008251401A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/06—Lysis of microorganisms
    • C12N1/066—Lysis of microorganisms by physical methods
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N13/00—Treatment of microorganisms or enzymes with electrical or wave energy, e.g. magnetism, sonic waves
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M41/00—Means for regulation, monitoring, measurement or control, e.g. flow regulation
    • C12M41/46—Means for regulation, monitoring, measurement or control, e.g. flow regulation of cellular or enzymatic activity or functionality, e.g. cell viability

Definitions

  • Methods are provided for differential extraction of DNA from at least two different cell types.
  • Systems for carrying out the differential extraction methods are also provided.
  • Forensic DNA analysis of sexual assault evidence often involves analysis of DNA from sperm cells and DNA from other cells such as epithelial cells.
  • the samples obtained from victims often contain a mixture of sperm and other cells such as epithelial cells. Because other cells such as epithelial cells may outnumber sperm cells by many folds, contamination from one or more other sources of DNA may occur while sperm DNA is being extracted. Therefore, it is often desirable to separate the sperm cells and epithelial cells, or separate the sperm DNA from the epithelial DNA as much as possible, prior to analysis. In certain instances, separation and isolation of a particular DNA to create an accurate profile is important for identification of an assailant.
  • Differential extraction is a broad term used to describe several extraction methods that can be used to separate cells.
  • unique characteristics of sperm cells allow for the differential extraction of the epithelial cells from the sperm cells.
  • One differential extraction procedure was described in 1985 (Gill et al., (1985) Nature 318: 557-9).
  • separation of the sperm cell fraction from the victim's DNA profile decreases ambiguity in the results and allows for easier interpretation of the perpetrator's DNA profile in a rape case.
  • a system for differential extraction of sperm cells comprises a plurality of compartments, wherein at least one compartment comprises a selective sperm lysis buffer.
  • the system comprises a first compartment comprising a cell-trapping matrix and a second compartment comprising a selective sperm lysis buffer.
  • the system further comprises a third compartment comprising a plurality of DNA-binding particles.
  • the system further comprises a fourth compartment comprising an elution buffer.
  • a system for differential extraction of sperm cells comprises a first compartment comprising a cell-trapping matrix; a second compartment comprising a cell wash buffer, a third compartment comprising a selective sperm lysis buffer; a fourth compartment comprising a plurality of DNA binding particles; a fifth compartment comprising a DNA wash buffer; and a sixth compartment comprising an elution buffer.
  • the system further comprises a seventh compartment comprising a DNA-binding buffer.
  • the seventh compartment further comprises a second plurality of DNA-binding particles.
  • the system further comprises an eighth compartment comprising a second plurality of DNA-binding particles.
  • the system comprises a plurality of compartment, wherein the plurality of compartments are part of a removable cartridge.
  • a method of differential extraction of sperm cells in a biological sample that comprises sperm cells and non-sperm cells comprises (a) placing the biological sample in a first compartment of a system, wherein the first compartment comprises a cell-trapping matrix; (b) capturing the sperm cells and the non-sperm cells with the cell-trapping matrix; (c) incubating the cell-trapping matrix and the captured sperm cells and non-sperm cells in a selective sperm lysis buffer to form a sperm cell lysate; (d) binding sperm cell DNA from the sperm cell lysate to a plurality of DNA-binding particles; and (e) eluting the sperm cell DNA from the DNA-binding particles.
  • capturing the sperm cells and the non-sperm cells with the cell-trapping matrix comprises applying a magnetic force to the cell-trapping matrix.
  • incubating the cell-trapping matrix and the captured sperm cells and non-sperm cells in a selective sperm lysis buffer occurs in the first compartment of the system.
  • the binding the sperm cell DNA to a plurality of DNA-binding particles occurs in a second compartment of the system.
  • eluting the sperm cell DNA from the DNA-binding particles occurs in the second compartment of the system.
  • the sperm cell lysate is moved from the first compartment to the second compartment.
  • incubating the cell-trapping matrix and the captured sperm cells and non-sperm cells in a selective sperm lysis buffer occurs in a second compartment of the system.
  • binding the sperm cell DNA to a plurality of DNA-binding particles occurs in a second compartment of the system.
  • eluting the sperm cell DNA from the DNA-binding particles occurs in a third compartment of the system.
  • the cell-trapping matrix and the captured sperm cells and non-sperm cells are moved from the first compartment to the second compartment using a magnetic force.
  • the non-sperm cells remain captured on the cell-trapping matrix after incubating the cell-trapping matrix in the selective sperm lysis buffer. In certain embodiments, the non-sperm cells are lysed and the non-sperm cell DNA is bound to the cell-trapping matrix. In certain embodiments, the non-sperm cells are lysed and the non-sperm cell DNA is bound to a second plurality of DNA-binding particles.
  • FIG. 1 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 1 involves transfer of fluids between compartments.
  • the system of FIG. 1 does not lyse the non-sperm cells, but instead collects residual DNA present in the sample after cell capture on the cell-trapping matrix.
  • FIG. 2 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 2 involves transfer of fluids between compartments.
  • the system of FIG. 2 uses the cell-trapping matrix as the DNA-binding particles for the non-sperm cell DNA.
  • FIG. 3 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 3 involves transfer of fluids between compartments.
  • the system of FIG. 3 comprises two separate compartments of DNA-binding particles.
  • FIG. 4 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 4 involves the transfer of particles and, in some instances, liquid between compartments.
  • the cell-trapping matrix is used as the DNA-binding matrix for the non-sperm cell DNA in the system shown in FIG. 4 .
  • FIG. 5 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 5 involves the transfer of particles between compartments.
  • the cell-trapping matrix is used as the DNA-binding matrix for the non-sperm cell DNA in the system shown in FIG. 5 .
  • FIG. 6 shows an exemplary system for differential extraction of sperm cell DNA and non-sperm cell DNA according to certain embodiments.
  • the system of FIG. 6 stores the DNA-binding particles separately from the DNA-binding buffer.
  • biological sample refers to any sample that contains at least one biological material.
  • biological materials include, but are not limited to, blood, saliva, skin, feces, urine, sperm cells, epithelial cells (including, but not limited to, vaginal epithelial cells), muscle tissue, and bone.
  • a cartridge refers to a system that comprises a plurality of compartments and does not contain sufficient fluid and/or magnetic particle handling mechanisms to function independently of a separate fluid-handling and/or magnetic particle-handling instrument.
  • a cartridge may be, in certain embodiments, designed for a single use, after which it is discarded.
  • one or more of the compartments in a cartridge contains a reagent.
  • all of the compartments of a cartridge are contained in a single unit.
  • the compartments of a cartridge are divided between two or more units that together form the cartridge.
  • a single cartridge is designed to process 1, 2, 4, 6, 8, 12, 16, 24, 48, 96 or more than 96 samples.
  • a cartridge is designed to process between 1 and 48 samples, or between 1 and 24 samples, or between 2 and 24 samples, or between 1 and 16 samples, or between 2 and 16 samples. In certain embodiments, when a cartridge is designed to process at least two samples, it is designed to process at least two of the samples simultaneously. In certain embodiments, a cartridge is designed to process all of the samples simultaneously.
  • cell mixture refers to a heterogeneous collection of at least two or more different cell types.
  • cell-trapping matrix refers to a matrix that captures cells, including but not limited to, sperm cells and epithelial cells. Certain exemplary cell trapping matrices are described, e.g., in U.S. Provisional Application No. 60/890,460. In certain embodiments, a cell-trapping matrix captures cells but does not bind DNA in the presence of a cell wash buffer, but is capable of binding DNA in a DNA-binding buffer.
  • cell wash buffer refers to a buffer in which cells are captured by a cell-trapping matrix but are not lysed. In certain embodiments, DNA does not bind to a cell-trapping matrix in the presence of a cell wash buffer.
  • Exemplary cell wash buffers include, but are not limited to, phosphate buffered saline (PBS); Tris-EDTA (TE), pH 7.5; Tris-Acetate-EDTA (TAE), pH 8.5); and Tris-Boric acid-EDTA (TBE), pH 8.
  • PBS phosphate buffered saline
  • Tris-EDTA TE
  • Tris-Acetate-EDTA TAE
  • TBE Tris-Boric acid-EDTA
  • compartment refers to any containment structure that defines a discrete space configured to hold fluid.
  • a compartment may be a stand-alone container or receptacle that defines an interior space configured to hold fluid.
  • a compartment may be one of a plurality of partitioned spaces within a container or receptacle, which is configured to hold fluid.
  • the fluid-holding space defined by a compartment may be substantially enclosed or alternatively, open, at least partially, to atmosphere.
  • differential extraction refers to extraction methods utilized to extract a subset of cell types from a heterogeneous population of cells.
  • differential extraction includes the selective lysis of sperm cells in a mixture of sperm cells and non-sperm cells, including, but not limited to, epithelial cells.
  • DNA-binding particles refers to magnetic particles that are capable of binding DNA under appropriate buffer conditions.
  • Exemplary magnetic particles include, but are not limited to, ferromagnetic, paramagnetic, and superparamagnetic particles.
  • DNA-binding particles bind DNA in the presence of a DNA-binding buffer.
  • DNA-binding buffer refers to a buffer in which DNA-binding particles and/or a cell-trapping matrix is capable of binding DNA.
  • selective sperm lysis buffer refers to a buffer that is capable of preferentially lysing sperm cells in a mixture comprising sperm cells and at least one type of non-sperm cells. Certain exemplary selective sperm lysis buffers are described, e.g., in U.S. Provisional Application Nos. 60/899,106 and 60/890,470. “Preferentially lysing sperm cells” means that primarily sperm cells are lysed. In certain embodiments, a negligible amount of non-sperm cells are lysed. In various embodiments, at least 80%, 85%, 90%, 95%, or 99% of the sperm cells are lysed. In various embodiments, at least 80%, 85%, 90%, or 95% of the non-sperm cells are not lysed.
  • Dilution buffer refers to a buffer that can be used to dilute a selective sperm lysis buffer so that it becomes a DNA binding buffer.
  • Dilution buffers may comprise, in various embodiments, a chaotropic salt, a monovalent salt, and/or an alcohol.
  • elution buffer refers to a buffer that releases DNA from DNA-binding particles and/or cell-trapping matrix.
  • Certain exemplary elution buffers include, but are not limited to, low-salt buffers (including, but not limited to, TE and deionized water).
  • low-salt buffers including, but not limited to, TE and deionized water.
  • one skilled in the art can select a suitable elution buffer according to the DNA binding particles and/or cell-trapping matrix being used.
  • heat is applied to facilitate elution of DNA in the presence of an elution buffer.
  • forensic sample refers to a biological sample obtained for use to address identity issues arising in legal contexts, including, but not limited to murder, rape, trauma, assault, battery, theft, burglary, other criminal matters, identity, parental or paternity testing, and mixed-up samples.
  • general lysis buffer refers to a buffer that lyses non-sperm cells and may or may not also lyse sperm cells. Certain exemplary general lysis buffers are known in the art, and in various embodiments, one skilled in the art can select a general lysis buffer based on the intended use.
  • a nonlimiting exemplary general lysis buffer comprises 2% SDS, 20 mM EDTA, 200 mM NaCl, 20 mM Tris (pH8), and 500 ⁇ g/mL proteinase K.
  • lysate refers to a liquid phase with lysed cell debris and DNA.
  • medical sample refers to a sample obtained to address medical issues including, but not limited to research, diagnosis, and tissue and organ transplants.
  • salt or “salt reagent” or “salt solution” refer to positively and/or negatively charged ionic reagents.
  • a salt reagent disrupts sperm chromatin.
  • a salt reagent may, in various embodiments, be a monovalent, bivalent, or multivalent ion.
  • Exemplary salt reagents include, but are not limited to LiCl, NaCl, KCl. Li 2 SO 4 , Na 2 SO 4 , K 2 SO 4 , MgCl 2 , CaCl 2 , MgSO 4 , CaSO 4 , NaNO 3 , KNO 3 , Mg(NO 3 ) 2 , and Ca(NO 3 ) 2 .
  • disulfide bond reducing agent refers to an agent that reduces disulfide bonds, e.g., in proteins. In certain embodiments, a disulfide bond reducing agent disrupts protamine disulfide bridges in sperm cells.
  • Disulfide bond reducing agents can be water-insoluble or water soluble. Exemplary water-insoluble agents include, but are not limited to, dithiothreitol (DTT) and Tris(2-carboxyethyl)phosphine hydrochloride (TCEP). Exemplary water-soluble agents include, but are not limited to, glutathione (GSH) and mercaptoethanol (ME).
  • a selective sperm lysis buffer comprises at least one disulfide bond reducing reagent and at least one salt reagent.
  • a disulfide bond reducing agent is selected from ME, DTT, GSH, and TCEP.
  • At least one salt reagent is selected from LiCl, NaCl, KCl. Li 2 SO 4 , Na 2 SO 4 , K 2 SO 4 , MgCl 2 , CaCl 2 , MgSO 4 , CaSO 4 , NaNO 3 , KNO 3 , Mg(NO 3 ) 2 , and Ca(NO 3 ) 2 . In certain embodiments, at least one salt reagent is selected from NaCl, KCl, and MgCl 2 .
  • a selective sperm lysis buffer comprises at least one salt reagent at a concentration of at least 0.1M, 0.25M, 0.5M, 1M, 1.5M, or 2M. In certain embodiments, a selective sperm lysis buffer comprises at least one salt reagent at a concentration of between 0.1M and 2M.
  • a selective sperm lysis buffer comprises at least one disulfide bond reducing reagent at a concentration of at least 0.01M, 0.05M, 0.1M, 0.2M, 0.3M, 0.4M, 0.5M, 0.7M or 0.8M.
  • a selective sperm lysis buffer comprises at least one disulfide bond reducing reagent selected from ME, DTT, GSH, and TCEP and at least one salt reagent selected from NaCl, KCl, MgCl 2 , and CaCl 2 .
  • the salt and reducing agent concentrations are such that the selective sperm lysis buffer will preferentially lyse sperm cells.
  • a selective sperm lysis buffer comprises NaCl. In certain embodiments, the NaCl concentration is at least 0.8M. In certain embodiments, a selective sperm lysis buffer comprises KCl. In certain embodiments, the KCl concentration is at least 0.8M. In certain embodiments, a selective sperm lysis buffer comprises MgCl 2 . In certain embodiments, the MgCl 2 concentration is at least 0.25M. In certain embodiments, a selective sperm lysis buffer comprises DTT at a concentration of at least 50 mM.
  • one of skill in the art can optimize the final salt concentration level to preferentially lyse sperm cells.
  • a selective sperm lysis buffer is diluted with a dilution buffer so that it becomes a DNA-binding buffer.
  • a selective sperm lysis buffer is diluted with a DNA-binding buffer and the resulting buffer is a DNA-binding buffer.
  • one skilled in the art can select an appropriate dilution buffer and/or appropriate dilution amount in order to create a DNA-binding buffer or maintain the DNA-binding properties of a DNA binding buffer after mixing with a selective sperm lysis buffer.
  • a cell-trapping matrix is a matrix that captures cells, including but not limited to, sperm cells and epithelial cells.
  • a cell-trapping matrix binds DNA under appropriate conditions, which conditions may be the same as, or different from, the conditions used to capture cells.
  • a cell-trapping matrix is comprised of magnetic particles. Exemplary magnetic particles include, but are not limited to, ferromagnetic, paramagnetic, and superparamagnetic particles.
  • Exemplary cell-trapping matrices and/or DNA-binding particles include, but are not limited to, porous silica beads with supermagnetic cores.
  • Exemplary porous silica beads with supermagnetic cores include, but are not limited to, MP-50 (6.5 ⁇ m) and MP-85 (>8 ⁇ m) (W.R. Grace, Columbia, Md.); DNA IQTM silica particles (Promega, Madison, Wis.); MagPrep® silica particles (Novagen, San Diego, Calif.); BcMag® silica-modified magnetic beads (5 ⁇ m or 1 ⁇ m) (Bioclone Inc., San Diego, Calif.); and supermagnetic silica particles (1 ⁇ m or 0.75 ⁇ m, G.
  • Certain exemplary non-silica cell-trapping matrices include, but are not limited to, iron oxide immobilized with streptavidin (Sigma, St. Louis, Mo.), iron(III) oxide powder (5 ⁇ m) (Sigma), MagMAX® magnetic particles (1 ⁇ m, Applied Biosystems, Foster City, Calif.); and Dynabeads® (Invitrogen, Carlsbad, Calif.), which may comprise different types of surface functional groups (e.g., Dynabeads® MyOne carboxylic acid beads, Dynabeads® WCX, Dynabeads® TALON, and Dynabeads® MyOne tosylactivated).
  • surface functional groups e.g., Dynabeads® MyOne carboxylic acid beads, Dynabeads® WCX, Dynabeads® TALON, and Dynabeads® MyOne tosylactivated.
  • a cell-trapping matrix comprises magnetic particles. In certain embodiments, the cell-trapping matrix captures cells in the absence of a magnetic field. In certain embodiments, the cell-trapping matrix captures cells in the presence of a magnetic field. The timing and mechanism of cell capture depends, in various embodiments, on the cell-trapping matrix used and the buffer conditions.
  • a cell trapping matrix may capture cells by any of a variety of mechanisms.
  • a cell-trapping matrix captures cells through a non-covalent interaction.
  • Certain exemplary non-covalent interactions include, but are not limited to, hydrogen bonding, cation- ⁇ interactions, ⁇ - ⁇ interactions, ionic pairing, hydrophobic interactions, dipole-dipole interactions, dipole-induced dipole interactions, charge-dipole interactions, and van Der Waals interactions.
  • cells are captured by the cell-trapping matrix through ionic interactions.
  • cells are captured by the cell-trapping matrix through an antibody/antigen interaction.
  • the duration and strength of the non-covalent interaction is such that cells remain captured by the cell-trapping matrix while the matrix is moved from one location to another.
  • the cell-trapping matrix comprises magnetic particles and the movement is caused by applying a magnetic field.
  • the type, duration and strength of a non-covalent association between cells and a cell-trapping matrix is determined, in various embodiments, by the size, shape, surface properties, surface morphologies, and/or density of the matrix; the size, shape, surface properties, surface morphologies, and/or density of the captured cells; and/or the composition, pH, and/or temperature of the buffer.
  • a cell-trapping matrix physically traps cells, e.g., when a magnetic field is applied. Such physical trapping may be, in certain embodiments, due to aggregation of cell-trapping matrix particles in the magnetic field.
  • a cell-trapping matrix comprises irregularly shaped particles to facilitate such physical trapping of cells.
  • the cell-trapping matrix particles may be smaller or larger than the cells to be captured, or may be larger than some cells and smaller than other cells to be captured.
  • the cell-trapping matrix may capture cells by pushing the cells towards the source of the magnetic field, sequestering them from the supernatant.
  • the cell-trapping matrix is comprised of particles at a density such that the spacing between particles is smaller than the size of the smallest cell in the sample.
  • more than one type of non-covalent interaction exists between cells and a cell-trapping matrix.
  • one type of non-covalent interaction may contribute more to cell capture, and which interaction predominates may vary from cell type to cell type in a sample.
  • sperm cells have a diameter of about 5 ⁇ m
  • epithelial cells have a diameter of about 50 ⁇ .
  • a cell-trapping matrix used to capture sperm cells and epithelial cells comprises particles with a diameter of between 0.5 ⁇ m and 100 ⁇ m.
  • the particles have a diameter of between 1 ⁇ m and 10 ⁇ m.
  • at least 85%, at least 90%, at least 95%, or at least 99% of the particles in a cell-trapping matrix have a diameter of between 0.5 ⁇ m and 100 ⁇ m, or between 1 ⁇ m and 10 ⁇ m.
  • One skilled in the art can, in various embodiments, select the appropriate particles size, shape, density and surface properties for capturing cells according to the particular application.
  • a cell-trapping matrix comprises one or more antibodies. In certain such embodiments, one or more of the antibodies binds a cell surface antigen present on at least one type of cell in a sample. In certain embodiments, a cell-trapping matrix comprises one or more antibodies that together bind to at least one cell surface antigen on two or more cell types in a sample. As a non-limiting example, in certain embodiments, a cell-trapping matrix may comprise a first set of particles coated with an antibody that binds a cell-surface antigen on epithelial cells and a second set of particles coated with an antibody that binds a cell-surface antigen on sperm cells.
  • Certain exemplary antibodies that bind sperm cells and/or epithelial cells include, but are not limited to, monoclonal antibody BerEP4, which binds the human epithelial antigen, EpCAM (epithelial cell adhesion molecule); antibodies to sperm protamine; antibodies to carbohydrate epitope located on human sperm agglutination antigen-I (SAGA-I) (see, e.g., U.S. Pat. No. 5,605,803); antibodies to SPAN-X, a sperm protein present in nuclear vacuoles and sperm nuclear redundant membranes (see, e.g., PCT/US99/24973); antibodies to C58 or SMARC32 (see, e.g., U.S. Published App. 2002/0182751).
  • an antibody binds a cell surface antigen (e.g., a protein or carbohydrate) present on multiple cell types.
  • cells are pushed, dragged, or carried by the cell-trapping matrix to the bottom of a compartment, when a magnetic field is applied underneath the compartment. In certain embodiments, cells are pushed, dragged, or carried by the cell-trapping matrix to the side of the compartment, when a magnetic field is applied from the side of the compartment. In certain embodiments, cells are pushed, dragged, or carried by the cell-trapping matrix to a magnetic bar inserted into the compartment. In certain such embodiments, the magnetic bar is covered, e.g., with a removable protectant to prevent contamination of the magnetic bar. In certain embodiments, the magnetic bar can be used to transfer the cell-trapping matrix from one compartment to another.
  • Dynabeads® MyOne Carboxylic Acid beads are used as a cell-trapping matrix to capture cells.
  • the particles are 1 ⁇ m and are used, in certain embodiments, at a density of about 10 6 particles/ ⁇ l for a sample comprising about 55 cells/ ⁇ L (e.g., 200 ⁇ L containing about 1000 sperm cells and about 10,000 epithelial cells). In certain embodiments, more that 10 6 particles/ ⁇ l can be used. In certain embodiments, fewer than 10 6 particles/ ⁇ l are used.
  • At least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the intact cells in a sample are captured by the cell-trapping matrix.
  • at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the remaining intact cells in a sample are captured, or remain captured, by the cell-trapping matrix.
  • a DNA-binding buffer when the DNA-binding particles are silica beads, a DNA-binding buffer comprises a chaotropic salt.
  • Certain exemplary chaotropic salts include, but are not limited to, guanidium isothiocyanate (GuSCN) and guanidium chloride.
  • a DNA-binding buffer when the DNA-binding particles are non-silica beads, a DNA-binding buffer comprises a chaotropic salt and alcohol.
  • the DNA-binding buffer further comprises a monovalent salt.
  • Certain exemplary monovalent salts include, but are not limited to, sodium acetate, sodium chloride, potassium acetate, potassium chloride, ammonium acetate, and ammonium chloride.
  • Certain exemplary alcohols include, but are not limited to, isopropanol and ethanol. In certain embodiments, the alcohol is at a concentration of 30% or greater in the DNA-binding buffer.
  • a DNA-binding buffer that comprises a chaotropic salt and an alcohol is referred to as a “DNA precipitation buffer.”
  • Certain exemplary DNA-binding buffers are described, e.g., in U.S. Pat. Nos. 5,234,809; 5,523,231; and 5,705,628. One skilled in the art can select a suitable DNA-binding buffer according to the DNA binding particles and/or cell-trapping matrix being used.
  • Exemplary DNA-binding buffers suitable for silica-based DNA-binding particles include, but are not limited to, BloodPrepTM DNA purification solution (Applied Biosystems) and DNA IQTM Lysis Solution (Promega).
  • Applied Biosystems BloodPrepTM DNA purification solution
  • DNA IQTM Lysis Solution Promega
  • one skilled in the art can add a suitable amount of an alcohol to the BloodPrepTM DNA purification solution (Applied Biosystems) or the DNA IQTM Lysis Solution (Promega).
  • isopropanol is added to one of those solutions to a final concentration of 30% to create a DNA precipitation buffer.
  • ethanol is added to one of those solutions to a final concentration of 40-50% to create a DNA precipitation buffer.
  • DNA-binding particles are stored in DNA binding buffer in the systems described herein. In certain embodiments, DNA-binding particles are stored separately from a DNA-binding buffer in the systems described herein. DNA-binding particles are stored separately, in certain embodiments, when the DNA binding buffer is a DNA precipitation buffer.
  • non-sperm cells are lysed in a DNA-binding buffer. In certain embodiments, non-sperm cells are lysed in a DNA-binding buffer with the application of heat. In certain embodiments, when a DNA-binding buffer is a DNA precipitation buffer, non-sperm cells are first lysed in a DNA-binding buffer without the alcohol. In certain embodiments, alcohol is then added to the lysate to create the DNA precipitation buffer.
  • a DNA wash buffers is formulated such that substantially no genomic DNA dissolves in the DNA wash buffer. In certain embodiments, a DNA wash buffers is formulated such that substantially no large DNA (e.g., greater than about 1 kb) dissolves in the DNA wash buffer.
  • Certain exemplary DNA wash buffers are known in the art and generally comprise at least one alcohol. Certain exemplary alcohols that may be used in DNA wash buffers include, but are not limited to, ethanol and isopropanol.
  • a DNA wash buffer when one DNA wash buffer is used, it comprises 90% ethanol. In certain embodiments, when the DNA is washed twice, the same DNA wash buffer is used for both washed. In certain embodiments, when the DNA is washed twice, two different DNA wash buffers are used. In certain embodiments, when two different DNA wash buffers are used, the second DNA wash buffer comprises a higher alcohol concentration than the first DNA wash buffer. In certain embodiments, a DNA wash buffer comprises GuSCN and/or GuCl. In certain embodiments, a DNA wash buffer comprises GuSCN and isopropanol. In certain embodiments, a DNA wash buffer comprises 70% ethanol. In certain embodiments, a DNA wash buffer comprises 90% ethanol.
  • one skilled in the art can formulate one or more DNA wash buffers according to the selected application.
  • RFLP Restriction Fragment Length Polymorphism
  • PCR Polymerase Chain Reaction
  • PCR Polymerase Chain Reaction
  • PCR refers to a reaction that can be used to amplify nucleic acids, including, but not limited to, small amounts of DNA.
  • PCR is a technique in which cycles of denaturation, annealing with one or more primers, and extension with one or more DNA polymerases, are used to create additional copies of a target DNA.
  • PCR amplifies the DNA sequence by more than 10 6 fold.
  • Certain exemplary methods of PCR are described, e.g., in U.S. Pat. Nos. 4,683,195; 4,965,188; and 4,683,202; and European Patent Nos. EP 201184 and EP 200362.
  • DNA samples are subjected to PCR amplification using primers specific for each locus that contains, e.g., an STR of interest.
  • An STR locus is composed of tandemly repeated sequences, each of which is, e.g., 2 to 7 bp in length.
  • loci containing 4 bp (tetranucleotide) and/or 5 bp repeat sequences are used for human identification. Four and 5 bp repeat sequences are found throughout the human genome and are, in certain instances, highly polymorphic.
  • the number of alleles at a tetranucleotide repeat STR locus ranges, in various embodiments, from about 4 to 20.
  • the amplified alleles from the individual DNA samples can be compared to one or more size standards, e.g., commercial DNA markers and/or locus-specific allelic ladders, to determine the alleles present at each locus.
  • size standards e.g., commercial DNA markers and/or locus-specific allelic ladders
  • allelic ladders comprise two or more distinct lengths of DNA representing two or more known alleles from a particular locus.
  • DNA may be visualized by any technique, including, but not limited to, silver staining, radioactive labeling, fluorescent labeling, various dyes and stains.
  • DNA is separated using denaturing or native gel electrophoresis, or any other size separation method.
  • amplified alleles are subjected to DNA sequence analysis.
  • a differential extraction system comprises a magnetic particle handling instrument and a removable cartridge comprising a plurality of compartments, wherein at least one of the compartments comprises at least one reagent used in the differential extraction system.
  • a magnetic particle handling instrument is similar to the BioRobot EZ1 Workstation (Qiagen). See, e.g., EZ1 DNA Handbook, Second Edition (February 2004) (Qiagen).
  • the BioRobot EZ1 Workstation comprises a stage capable of moving in a plane parallel to the floor, a pipette capable of moving upwards and downwards relative to the stage, and a magnet capable of moving towards and away from the pipette.
  • the BioRobot EZ1 Workstation is able to move both magnetic particles and liquids between compartments.
  • the BioRobot EZ1 Workstation functions as follows.
  • a removable cartridge containing a plurality of compartments comprising a plurality of liquid reagents is placed on the stage of the BioRobot EZ1 Workstation.
  • the removable cartridge also comprises at least one compartment containing magnetic particles.
  • the stage moves the compartment containing the magnetic particles to a position beneath the pipette.
  • the pipette lowers into the compartment and sucks up a liquid solution containing the magnetic particles.
  • the magnet moves toward the pipette to hold the magnetic particles inside the pipette while the pipette expels the liquid solution without the magnetic particles.
  • the stage then moves a second compartment containing a reagent to a position beneath the pipette containing the magnetic particles held by the magnet.
  • the pipette sucks up the reagent from the second compartment, the magnet moves away from the pipette and the pipette expels the reagent and the magnetic particles into the second compartment.
  • a magnetic particle handling instrument is similar to the Maxwell 16 Instrument (Promega). See, e.g., Maxwell 16 Instrument Operating Manual (September 2005) (Promega).
  • the Maxwell 16 Instrument comprises a stage capable of moving in a plane parallel to the floor, a plunger capable of moving upwards and downwards relative to the stage, and a magnet located inside of the plunger and capable of moving upwards and downwards relative to the end of the plunger.
  • the Maxwell 16 Instrument is able to move magnetic particles, but not liquids, between compartments.
  • the Maxwell 16 Instrument functions as follows. A removable cartridge containing a plurality of compartments comprising a plurality of liquid reagents is placed on the stage of the Maxwell 16 Instrument.
  • the removable cartridge also comprises at least one compartment containing magnetic particles.
  • the stage moves the compartment containing the magnetic particles to a position beneath the plunger.
  • the plunger pipette lowers into the compartment and the magnet lowers within the plunger to attract the magnetic particles to the end of the plunger.
  • the plunger and magnet then rise, and the stage moves a second compartment containing a reagent to a position beneath the plunger with the magnetic particles held by the magnet.
  • the plunger lowers into the second compartment and the magnet rises away from the end of the plunger, releasing the magnetic particles into the second compartment.
  • a magnetic particle handling instrument comprises a stage capable of moving in a plane parallel to the floor, a pipette capable of moving upwards and downwards relative to the stage, and a magnet in a location allowing it to contact a cartridge placed on the stage.
  • a magnet may be located beneath the cartridge or on one or multiple sides of the cartridge.
  • the magnet is capable of moving towards and away from the cartridge in order to exert and release a magnetic force on at least one compartment of the cartridge.
  • the magnet is stationery and can be turned on and off electronically in order to exert and release a magnetic force on at least one compartment of the cartridge.
  • a removable cartridge containing a plurality of compartments comprising a plurality of liquid reagents is placed on the stage of the instrument.
  • the removable cartridge also comprises at least one compartment containing magnetic particles.
  • the stage moves a compartment containing a reagent to a position beneath the pipette.
  • the pipette sucks up the reagent and the stage moves the compartment containing the magnetic particles to a position beneath the pipette.
  • the pipette then expels the reagent into the compartment.
  • the magnet attracts the magnetic particles to one location within the compartment, away from the pipette, and the pipette then sucks up the liquid without the magnetic particles.
  • the pipette can be used to bring reagents to the magnetic particles and remove reagents from the magnetic particles, while a magnet is used to hold the magnetic particles out of the way of the pipette.
  • one skilled in the art can design and/or program an instrument to carry out the methods described herein.
  • an instrument may be similar to one or more of the instruments described above.
  • a system for differential extraction comprises a cartridge comprising a plurality of compartments, wherein at least one of the compartments comprises a selective sperm lysis buffer. Certain exemplary systems and methods for differential extraction are described herein.
  • the method comprises transferring fluids between compartments.
  • the method comprises transferring DNA-binding particles between compartments.
  • the method comprises transferring fluids and DNA-binding particles between compartments.
  • differential extraction systems are non-limiting.
  • the arrangement of compartments shown in the Figures and described herein is figurative and non-limiting.
  • one skilled in the art can design a system based on the teachings herein, the intended use, and the selected instrumentation.
  • such a system comprises more or fewer compartments than any of the following exemplary systems described herein.
  • such a system separates reagents into separate compartments that are shown combined in one or more of the following exemplary systems.
  • FIG. 1 shows a first non-limiting exemplary system for differential extraction of sperm cells and non-sperm cells, e.g., epithelial cells, according to certain embodiments.
  • the system shown in FIG. 1 is used, for example, when a sample comprises an excess of non-sperm cells relative to sperm cells (e.g., at least 10-fold more non-sperm cells than sperm cells).
  • the system of FIG. 1 does not lyse the non-sperm cells, but instead collects residual DNA present in the sample after cell capture on the cell-trapping matrix. Such residual DNA may be present due to cell breakage prior to placing the sample in the system.
  • Such cell breakage may occur, in various embodiments, prior to collection, during collection, during storage, during transport, and/or during transfer of the sample from one container to another. Because of the excess of non-sperm cells relative to sperm-cells in the sample, the residual DNA comprises an excess of non-sperm cell DNA relative to sperm cell DNA.
  • a sample comprising a mixture of sperm cells and non-sperm cells is placed in compartment 1 .
  • Compartment 1 comprises a cell-trapping matrix, which captures the sperm cells and the non-sperm cells.
  • the supernatant from compartment 1 is then removed to a collection vessel (not shown). If the original sample contained an excess of non-sperm cells, e.g., epithelial cells, relative to sperm cells (for example, more than 10-fold more non-sperm cells than sperm cells), the supernatant from the sample binding may contain sufficient non-sperm cell DNA for analysis.
  • a cell wash buffer located in compartment 2 is then transferred to compartment 1 .
  • the cell wash supernatant from compartment 1 is then transferred to a waste receptacle, which is shown as compartment 0 .
  • the waste receptacle may or may not be a contiguous part of the system shown in FIG. 1 .
  • the waste compartment 0 is not part of the cartridge.
  • a cartridge comprises compartments 0 through 6 of FIG. 1 .
  • a selective sperm lysis buffer is transferred from compartment 3 to compartment 1 .
  • the selective sperm lysis buffer lyses the sperm cells bound to the cell-trapping matrix in compartment 1 .
  • the lysate supernatant is transferred from compartment 1 to compartment 4 , which contains DNA-binding particles and a dilution buffer, which, when combined with the selective sperm lysis buffer, forms a DNA-binding buffer.
  • the supernatant from compartment 4 is transferred to the waste compartment 0 .
  • a DNA wash buffer is then transferred from compartment 5 to compartment 4 .
  • the DNA wash buffer supernatant is then transferred from compartment 4 to the waste compartment 0 .
  • a second DNA wash buffer is contained in a compartment 7 (not shown in FIG. 1 ). In certain such embodiments, the second DNA wash buffer is then transferred to compartment 4 . The second DNA wash buffer supernatant is then transferred from compartment 4 to the waste compartment 0 .
  • an elution buffer is transferred from compartment 6 to compartment 4 .
  • the elution buffer releases sperm cell DNA from the DNA-binding particles into the elution supernatant.
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant may then transferred from compartment 4 to a second collection vessel (not shown in FIG. 1 ). The sperm cell DNA can then be subjected to DNA analysis.
  • FIG. 2 shows a second non-limiting exemplary system for differential extraction of sperm cells and non-sperm cells, e.g., epithelial cells, according to certain embodiments.
  • the cell-trapping matrix also serves as the DNA-binding matrix for the non-sperm cell DNA.
  • a sample comprising a mixture of sperm cells and non-sperm cells is placed in compartment 1 .
  • Compartment 1 comprises a cell-trapping matrix, which captures the sperm cells and the non-sperm cells.
  • the supernatant from compartment 1 is then transferred to a waste receptacle, which is shown as compartment 0 .
  • the waste receptacle may or may not be a contiguous part of the system shown in FIG. 2 .
  • the waste compartment 0 when the compartments 1 through 7 of FIG. 2 are contained in a cartridge, the waste compartment 0 is not part of the cartridge.
  • a cartridge comprises compartments 0 through 7 of FIG. 2 .
  • a cell wash buffer located in compartment 2 is then transferred to compartment 1 .
  • the cell wash supernatant from compartment 1 is then transferred to a waste receptacle, which is shown as compartment 0 .
  • a selective sperm lysis buffer is transferred from compartment 3 to compartment 1 .
  • the selective sperm lysis buffer lyses the sperm cells captured by the cell-trapping matrix in compartment 1 .
  • the lysate supernatant is transferred from compartment 1 to compartment 5 , which contains DNA-binding particles and a dilution buffer, which, when combined with the selective sperm lysis buffer, forms a DNA-binding buffer.
  • a DNA binding buffer is then transferred from compartment 4 to compartment 1 , which now contains non-sperm cells captured by the cell-trapping matrix.
  • the DNA-binding buffer is incubated with the cell-trapping matrix for five minutes with heating to about 70° C. (heating element not shown in FIG. 2 ) to lyse the non-sperm cells, e.g., epithelial cells.
  • the heating element is, in certain embodiments, part of a fluid handling or magnetic particle handling instrument.
  • Non-sperm cell DNA binds to the cell-trapping matrix in the DNA binding buffer.
  • compartments 1 and 5 Following DNA binding in compartments 1 and 5 , the supernatants from compartments 1 and 5 are transferred to the waste compartment 0 .
  • a DNA wash buffer is then transferred from compartment 6 to each of compartments 1 and 5 .
  • the DNA wash buffer supernatant is then transferred from compartments 1 and 5 to the waste compartment 0 .
  • a second DNA wash buffer is contained in a compartment 8 (not shown in FIG. 2 ). In certain such embodiments, the second DNA wash buffer is then transferred to compartments 1 and 5 . The second DNA wash buffer supernatant is then transferred from compartments 1 and 5 to the waste compartment 0 .
  • an elution buffer is transferred from compartment 7 to each of compartments 1 and 5 .
  • the elution buffer releases sperm cell DNA from the DNA-binding particles into the elution supernatant in compartment 5 and releases non-sperm cell DNA from the DNA-binding particles into the elution supernatant in compartment 1 .
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant is then transferred from compartment 5 to a collection vessel (not shown in FIG. 3 ).
  • the sperm cell DNA can then be subjected to DNA analysis.
  • the elution supernatant is then transferred from compartment 1 to a second collection vessel (not shown in FIG. 3 ).
  • the non-sperm cell DNA can then be subjected to DNA analysis.
  • FIG. 3 shows a third non-limiting exemplary system for differential extraction of sperm cells and non-sperm cells, e.g., epithelial cells, according to certain embodiments.
  • the system shown in FIG. 3 comprises two separate compartments containing DNA-binding particles, one of which is used to bind sperm cell DNA and one of which is used to bind non-sperm cell DNA.
  • a sample comprising a mixture of sperm cells and non-sperm cells is placed in compartment 1 .
  • Compartment 1 comprises a cell-trapping matrix, which captures the sperm cells and the non-sperm cells.
  • the supernatant from compartment 1 is then transferred to a waste receptacle, which is shown as compartment 0 .
  • the waste receptacle may or may not be a contiguous part of the system shown in FIG. 3 .
  • the waste compartment 0 when the compartments 1 through 7 of FIG. 3 are contained in a cartridge, the waste compartment 0 is not part of the cartridge.
  • a cartridge comprises compartments 0 through 7 of FIG. 3 .
  • a cell wash buffer located in compartment 2 is then transferred to compartment 1 .
  • the cell wash supernatant from compartment 1 is then transferred to a waste receptacle, which is shown as compartment 0 .
  • a selective sperm lysis buffer is transferred from compartment 3 to compartment 1 .
  • the selective sperm lysis buffer lyses the sperm cells captured by the cell-trapping matrix in compartment 1 .
  • the lysate supernatant is transferred from compartment 1 to compartment 5 , which contains DNA-binding particles and a dilution buffer, which, when combined with the selective sperm lysis buffer, forms a DNA-binding buffer.
  • a DNA binding buffer is then transferred from compartment 4 to compartment 1 , which now contains non-sperm cells captured by the cell-trapping matrix. While transferring the DNA-binding buffer from compartment 4 , in certain embodiments, the DNA-binding particles are held in compartment 4 by a magnet on the fluid handling instrument, to prevent the DNA-binding particles from being removed with the DNA-binding buffer.
  • the DNA-binding buffer is incubated with the cell-trapping matrix for five minutes with heating to about 70° C. (heating element not shown in FIG. 3 ) to lyse the non-sperm cells, e.g., epithelial cells.
  • the heating element is, in certain embodiments, part of a fluid handling or particle handling instrument.
  • the DNA-binding buffer/lysate supernatant is then transferred from compartment 1 back to compartment 4 , which contains DNA-binding particles.
  • compartments 4 and 5 Following DNA binding in compartments 4 and 5 , the supernatants from compartments 4 and 5 are transferred to the waste compartment 0 .
  • a DNA wash buffer is then transferred from compartment 6 to each of compartments 4 and 5 .
  • the DNA wash buffer supernatant is then transferred from compartments 4 and 5 to the waste compartment 0 .
  • a second DNA wash buffer is contained in a compartment 8 (not shown in FIG. 3 ). In certain such embodiments, the second DNA wash buffer is then transferred to compartments 4 and 5 . The second DNA wash buffer supernatant is then transferred from compartments 4 and 5 to the waste compartment 0 .
  • an elution buffer is transferred from compartment 7 to each of compartments 4 and 5 .
  • the elution buffer releases sperm cell DNA from the DNA-binding particles into the elution supernatant in compartment 5 and releases non-sperm cell DNA from the DNA-binding particles into the elution supernatant in compartment 4 .
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant may then transferred from compartment 5 to a collection vessel (not shown in FIG. 3 ).
  • the sperm cell DNA can then be subjected to DNA analysis.
  • the elution supernatant may then transferred from compartment 4 to a second collection vessel (not shown in FIG. 3 ).
  • the non-sperm cell DNA can then be subjected to DNA analysis.
  • a dilution buffer and/or a DNA-binding buffer is kept separate from DNA-binding particles in a system until the DNA-binding reaction is carried out. Keeping such components separate may be desirable, in certain embodiments, when the dilution buffer or DNA-binding buffer comprises alcohol.
  • the dilution buffer or DNA-binding buffer comprises alcohol.
  • One skilled in the art can modify any of the systems of FIGS. 1 to 3 to keep the DNA-binding particles separate from the dilution and/or DNA-binding buffer until the DNA-binding reaction is carried out.
  • a magnetic force is applied to the cell-trapping matrix to facilitate cell trapping.
  • the magnetic force is applied, in certain embodiments, by an instrument portion of the differential extraction system.
  • FIG. 4 shows a fourth non-limiting exemplary system for differential extraction of sperm cells and non-sperm cells, e.g., epithelial cells, according to certain embodiments.
  • the system shown in FIG. 4 is designed for a magnetic particle-handling instrument that is also able to move liquid between compartments. See, e.g., the BioRobot EZ1 Workstation (Qiagen).
  • the system shown in FIG. 4 processes sperm cell DNA in compartments 3 to 6 and non-sperm cell DNA in compartments 7 to 9 .
  • the cell-trapping matrix also serves as the DNA-binding matrix for the non-sperm cell DNA in the exemplary system shown in FIG. 4 .
  • the cell-trapping matrix in that system is magnetic.
  • a sample comprising a mixture of sperm cells and non-sperm cells is placed in compartment 1 .
  • Compartment 1 comprises a cell-trapping matrix, which captures the sperm cells and the non-sperm cells.
  • the cell-trapping matrix is transferred to compartment 2 , which contains a cell wash buffer.
  • the cell-trapping matrix is then transferred to compartment 3 , which contains a selective sperm lysis buffer.
  • the selective sperm lysis buffer lyses the sperm cells captured by the cell-trapping matrix.
  • the cell-trapping matrix which still has captured non-sperm cells, is transferred to the DNA-binding buffer in compartment 7 .
  • the DNA-binding buffer in compartment 7 is incubated with the cell-trapping matrix for five minutes with heating to about 70° C. (heating element not shown in FIG. 4 ) to lyse the non-sperm cells, e.g., epithelial cells.
  • the heating element is, in certain embodiments, part of a fluid handling or particle handling instrument.
  • the non-sperm cell DNA binds to the cell-trapping matrix in the DNA binding buffer.
  • the cell-trapping matrix with the bound non-sperm cell DNA is then transferred to compartment 8 , which contains a DNA wash buffer.
  • compartment 9 which contains an elution buffer.
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant may then transferred from compartment 9 to a collection vessel (not shown in FIG. 4 ).
  • the non-sperm cell DNA can then be subjected to DNA analysis.
  • the selective sperm lysis buffer supernatant in compartment 3 is transferred to compartment 4 , which contains DNA-binding particles and a dilution buffer, which, when combined with the selective sperm lysis buffer, forms a DNA-binding buffer.
  • the DNA-binding particles with the bound sperm cell DNA are then transferred to compartment 5 , which contains a DNA wash buffer.
  • the DNA-binding particles with the bound sperm cell DNA are transferred to compartment 6 , which contains an elution buffer.
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant may then transferred from compartment 6 to a second collection vessel (not shown in FIG. 4 ).
  • the sperm cell DNA can then be subjected to DNA analysis.
  • a second DNA wash buffer is contained in a compartment 10 and in a compartment 11 (not shown in FIG. 4 ).
  • the cell-trapping matrix with the bound non-sperm cell DNA is transferred to compartment 10 , which contains a second DNA wash buffer, prior to being transferred to the elution compartment.
  • the DNA-binding matrix with the bound sperm cell DNA is transferred to compartment 11 , which contains a second DNA wash buffer, prior to being transferred to the elution compartment.
  • FIG. 5 shows a fifth non-limiting exemplary system for differential extraction of sperm cells and non-sperm cells, e.g., epithelial cells, according to certain embodiments.
  • the system shown in FIG. 5 is designed for a magnetic particle-handling instrument that cannot also able to move liquid between compartments. See, e.g., the Maxwell 16 Instrument (Promega).
  • the system shown in FIG. 5 processes sperm cell DNA in compartments 3 to 5 and non-sperm cell DNA in compartments 6 to 8 .
  • the cell-trapping matrix also serves as the DNA-binding matrix for the non-sperm cell DNA in the exemplary system shown in FIG. 5 .
  • the cell-trapping matrix in that system is magnetic.
  • a sample comprising a mixture of sperm cells and non-sperm cells is placed in compartment 1 .
  • Compartment 1 comprises a cell-trapping matrix, which captures the sperm cells and the non-sperm cells.
  • the cell-trapping matrix is transferred to compartment 2 , which contains a cell wash buffer.
  • the cell-trapping matrix is then transferred to compartment 3 .
  • Compartment 3 in FIG. 5 comprises two sections that are partitioned from one another. The partition between the sections is breakable by the magnetic particle handling instrument, e.g., by physical force.
  • the top portion of compartment 3 comprises a selective sperm lysis buffer.
  • the bottom portion of compartment 3 which is partitioned from the top portion, contains DNA-binding particles and a dilution buffer.
  • the cell-trapping matrix is transferred into the top portion initially.
  • the selective sperm lysis buffer lyses the sperm cells captured by the cell-trapping matrix.
  • the cell-trapping matrix After lysis of the sperm cells, the cell-trapping matrix, which is still has captured non-sperm cells, is transferred to the DNA-binding buffer in compartment 6 .
  • the DNA-binding buffer is incubated with the cell-trapping matrix for five minutes with heating to about 70° C. (heating element not shown in FIG. 5 ) to lyse the non-sperm cells, e.g., epithelial cells.
  • the heating element is, in certain embodiments, part of a fluid handling or particle handling instrument.
  • the non-sperm cell DNA binds to the cell-trapping matrix in the DNA binding buffer.
  • the cell-trapping matrix with the bound non-sperm cell DNA is then transferred to compartment 7 , which contains a DNA wash buffer.
  • compartment 8 the cell-trapping matrix with the bound non-sperm cell DNA is transferred to compartment 8 , which contains an elution buffer.
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant may then transferred from compartment 8 to a collection vessel (not shown in FIG. 5 ).
  • the non-sperm cell DNA can then be subjected to DNA analysis.
  • the instrument breaks the breakable partition between the top portion compartment 3 and the bottom portion of compartment 3 to mix the selective sperm lysis buffer supernatant with the DNA-binding particles and the dilution buffer, which, when combined with the selective sperm lysis buffer, forms a DNA-binding buffer.
  • the DNA-binding particles with the bound sperm cell DNA are then transferred to compartment 4 , which contains a DNA wash buffer.
  • the DNA-binding particles with the bound sperm cell DNA are transferred to compartment 5 , which contains an elution buffer.
  • the elution buffer is heated to facilitate elution of the bound DNA.
  • the elution supernatant is then transferred from compartment 5 to a second collection vessel (not shown in FIG. 5 ).
  • the sperm cell DNA can then be subjected to DNA analysis.
  • a second DNA wash buffer is contained in a compartment 9 and in a compartment 10 (not shown in FIG. 5 ).
  • the cell-trapping matrix with the bound non-sperm cell DNA is transferred to compartment 9 , which contains a second DNA wash buffer, prior to being transferred to the elution compartment.
  • the DNA-binding matrix with the bound sperm cell DNA is transferred to compartment 10 , which contains a second DNA wash buffer, prior to being transferred to the elution compartment.
  • FIG. 6 shows a system similar to the system of FIG. 5 , except the DNA-binding particles used to bind the sperm cell DNA are kept in a separate compartment (compartment 4 ) from the dilution buffer, according to certain embodiments.
  • compartment 3 has two separate sections separated by a breakable seal, similar to compartment 3 of the system of FIG. 5 .
  • the lower compartment contains only the dilution buffer, so when the instrument breaks the seal, the selective sperm lysis buffer and the dilution buffer form a DNA-binding buffer. The instrument then transfers the DNA-binding particles from compartment 4 to compartment 3 to bind the sperm cell DNA.
  • a dilution buffer or a DNA-binding buffer is kept separate from DNA-binding particles in a system until the DNA-binding reaction is carried out. Keeping such components separate may be desirable, in certain embodiments, when the dilution buffer or DNA-binding buffer comprises alcohol. In various embodiments, one skilled in the art can modify any of the systems of FIGS. 3 to 6 to keep the DNA-binding particles separate from the dilution and/or DNA-binding buffer until the DNA-binding reaction is carried out.
  • a system comprises one or more empty compartments.
  • One or more empty compartments may be used, in certain embodiments, as a location to dry the DNA-binding particles, e.g., after a wash and before elution.

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US12/117,579 US8993292B2 (en) 2007-01-16 2008-05-08 Methods and systems for differential extraction
AU2008251401A AU2008251401A1 (en) 2007-05-09 2008-05-09 Methods and systems for differential extraction
JP2010507701A JP2010527442A (ja) 2007-05-09 2008-05-09 差次的抽出のための方法および系
BRPI0811304-1A2A BRPI0811304A2 (pt) 2007-05-09 2008-05-09 Processos e sistemas para extração diferencial
CN200880023150.7A CN101796179A (zh) 2007-05-09 2008-05-09 用于差异提取的方法和系统
EP08755249A EP2144993A4 (fr) 2007-05-09 2008-05-09 Procédés et systèmes pour extraction différentielle
CA002686842A CA2686842A1 (fr) 2007-05-09 2008-05-09 Procedes et systemes pour extraction differentielle
PCT/US2008/063273 WO2008141203A1 (fr) 2007-05-09 2008-05-09 Procédés et systèmes pour extraction différentielle
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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20160046927A1 (en) * 2007-01-16 2016-02-18 Applied Biosystems, Llc Methods and systems for differential extraction

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2171058A1 (fr) 2007-07-23 2010-04-07 Applied Biosystems Inc. Procédé de récupération d'acide nucléique de sperme d'un échantillon médicolégal
US9168028B2 (en) * 2007-10-23 2015-10-27 Lotus Bio (Nymphaea) Ltd Cartridge for a biological sample
US10865440B2 (en) * 2011-10-21 2020-12-15 IntegenX, Inc. Sample preparation, processing and analysis systems
CN105349525A (zh) * 2015-11-03 2016-02-24 四川农业大学 精子基因组dna的提取试剂及其方法

Citations (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5541072A (en) 1994-04-18 1996-07-30 Immunivest Corporation Method for magnetic separation featuring magnetic particles in a multi-phase system
WO2000077251A2 (fr) 1999-06-11 2000-12-21 Astrazeneca Uk Limited Dosages biologiques
WO2001012847A2 (fr) 1999-08-11 2001-02-22 Universiteit Gent Isolation de cellules dans des echantillons judiciaires pour empreintes genetiques
US6368800B1 (en) 1997-01-21 2002-04-09 Promega Corporation Kits for isolating biological target materials using silica magnetic particles
US20030038087A1 (en) 2000-01-24 2003-02-27 Garvin Alex M. Physical separation of cells by filtration
WO2003070898A2 (fr) 2002-02-19 2003-08-28 Choicepoint Asset Company Extraction selective d'adn de groupes de cellules
US20050019905A1 (en) * 2003-07-23 2005-01-27 The President And Fellows Of Harvard College System for containing and processing small objects
US20050032097A1 (en) 2003-06-17 2005-02-10 Garvin Alex M. Method for processing samples containing sperm and non-sperm cells for subsequent analysis of the sperm DNA
WO2006031591A2 (fr) 2004-09-10 2006-03-23 Promega Corporation Procedes et ensembles d'isolement de cellules du sperme
WO2008089280A2 (fr) 2007-01-16 2008-07-24 Applied Biosystems, Llc Lyse sélective de cellules de sperme

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5786182A (en) * 1997-05-02 1998-07-28 Biomerieux Vitek, Inc. Dual chamber disposable reaction vessel for amplification reactions, reaction processing station therefor, and methods of use
US8993292B2 (en) * 2007-01-16 2015-03-31 Applied Biosystems Llc Methods and systems for differential extraction

Patent Citations (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5541072A (en) 1994-04-18 1996-07-30 Immunivest Corporation Method for magnetic separation featuring magnetic particles in a multi-phase system
US6368800B1 (en) 1997-01-21 2002-04-09 Promega Corporation Kits for isolating biological target materials using silica magnetic particles
WO2000077251A2 (fr) 1999-06-11 2000-12-21 Astrazeneca Uk Limited Dosages biologiques
WO2001012847A2 (fr) 1999-08-11 2001-02-22 Universiteit Gent Isolation de cellules dans des echantillons judiciaires pour empreintes genetiques
US20030038087A1 (en) 2000-01-24 2003-02-27 Garvin Alex M. Physical separation of cells by filtration
WO2003070898A2 (fr) 2002-02-19 2003-08-28 Choicepoint Asset Company Extraction selective d'adn de groupes de cellules
US20050032097A1 (en) 2003-06-17 2005-02-10 Garvin Alex M. Method for processing samples containing sperm and non-sperm cells for subsequent analysis of the sperm DNA
US20050019905A1 (en) * 2003-07-23 2005-01-27 The President And Fellows Of Harvard College System for containing and processing small objects
WO2006031591A2 (fr) 2004-09-10 2006-03-23 Promega Corporation Procedes et ensembles d'isolement de cellules du sperme
WO2008089280A2 (fr) 2007-01-16 2008-07-24 Applied Biosystems, Llc Lyse sélective de cellules de sperme

Non-Patent Citations (14)

* Cited by examiner, † Cited by third party
Title
Extended European Search Report for EP Application No. 08755249.3, dated Jun. 25, 2010.
EZ1 DNA Handbook, Second Edition, Feb. 2004, 24 pages, www.giagen.com.
Forensic Science International, vol. 72, pp. 25-33 (1995).
Garvin, A. M. , "Filtration Based DNA Preparation for Sexual Assault Cases", Journal of Forensic Sciences, Callaghan and CO, Chicago vol. 48, No. 5, Sep. 1, 2003 , 1084-1087.
Gill, P. et al., "Forensic Application of DNA 'Fingerprints' Nature", Nature Publishing Group,London, vol. 318 No. 6046 pp. 577-578 Dec. 12, 1985.
Gill, P. et al., "Forensic Application of DNA ‘Fingerprints’ Nature", Nature Publishing Group,London, vol. 318 No. 6046 pp. 577-578 Dec. 12, 1985.
International Congress Series, vol. 1288, pp. 700-703 (2006).
International Search Report for Int'l appl. No. PCT/US08/063273 dated Sep. 3, 2008. Along with the Written Opinion of the International Searching Authority.
Legal Medicine, vol. 8, pp. 43-47 (2006).
Maxwell(TM) 16 datasheet, Profiles in DNA, Feb. 2006, www.promega.com, 3 pages.
Maxwell® 16 System datasheet, www.promega.com/maxwell16/dnaiq/, 4 pages, first available Nov. 15, 2006.
Maxwell™ 16 datasheet, Profiles in DNA, Feb. 2006, www.promega.com, 3 pages.
Technical Bulletin: DNA IQ (TM) Casework Sample Kit for Maxwell 16. Promega. Revised Oct. 2008. *
Written Opinion and International Preliminary Report on Patentability for PCT Application No. PCT/US2008/063273, mailed Nov. 19, 2009.

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20160046927A1 (en) * 2007-01-16 2016-02-18 Applied Biosystems, Llc Methods and systems for differential extraction

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CA2686842A1 (fr) 2008-11-20
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AU2008251401A1 (en) 2008-11-20
WO2008141203A1 (fr) 2008-11-20
BRPI0811304A2 (pt) 2014-12-30
US20080281089A1 (en) 2008-11-13
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CN101796179A (zh) 2010-08-04

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